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RXRG retinoid X receptor gamma [ Homo sapiens (human) ]

Gene ID: 6258, updated on 5-Apr-2020

Summary

Official Symbol
RXRGprovided by HGNC
Official Full Name
retinoid X receptor gammaprovided by HGNC
Primary source
HGNC:HGNC:10479
See related
Ensembl:ENSG00000143171 MIM:180247
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RXRC; NR2B3
Summary
This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the antiproliferative effects of retinoic acid (RA). This receptor forms dimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene is expressed at significantly lower levels in non-small cell lung cancer cells. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2010]
Expression
Broad expression in heart (RPKM 1.5), adrenal (RPKM 1.5) and 22 other tissues See more
Orthologs

Genomic context

See RXRG in Genome Data Viewer
Location:
1q23.3
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (165400922..165445355, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (165370159..165414592, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene LMX1A antisense RNA 2 Neighboring gene LMX1A antisense RNA 1 Neighboring gene LIM homeobox transcription factor 1 alpha Neighboring gene LRRC52 antisense RNA 1 Neighboring gene leucine rich repeat containing 52 Neighboring gene ribosomal protein S2 pseudogene 10

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study of personality traits in bipolar patients.
NHGRI GWA Catalog
Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03).
NHGRI GWA Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA Catalog
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef induces loss of F-actin assembly and inhibits retinoid receptor-mediated transcription PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
retinoic acid-responsive element binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to retinoic acid IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
host cell nucleus IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
retinoic acid receptor RXR-gamma
Names
nuclear receptor subfamily 2 group B member 3

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029517.2 RefSeqGene

    Range
    5230..49434
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001256570.1NP_001243499.1  retinoic acid receptor RXR-gamma isoform c

    See identical proteins and their annotated locations for NP_001243499.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes an additional exon in its 5' UTR, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c, also known as RXRgamma2) is shorter at the N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
    Source sequence(s)
    AB593016, AL160058, BE349162, DA251671
    Consensus CDS
    CCDS72970.1
    UniProtKB/TrEMBL
    A0A087WZ88, F1T097
    Related
    ENSP00000482458.1, ENST00000619224.1
    Conserved Domains (2) summary
    cd06943
    Location:110318
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:1490
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
  2. NM_001256571.2NP_001243500.1  retinoic acid receptor RXR-gamma isoform c

    See identical proteins and their annotated locations for NP_001243500.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate internal promoter, and it thus differs in the 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c, also known as RXRgamma2) is shorter at the N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
    Source sequence(s)
    BC012063, BE349162, BI768747, DA893476
    Consensus CDS
    CCDS72970.1
    UniProtKB/Swiss-Prot
    P48443
    UniProtKB/TrEMBL
    A0A087WZ88
    Conserved Domains (2) summary
    cd06943
    Location:110318
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:1490
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
  3. NM_006917.5NP_008848.1  retinoic acid receptor RXR-gamma isoform a

    See identical proteins and their annotated locations for NP_008848.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a, also known as RXRgamma1).
    Source sequence(s)
    BC012063, BE349162, DA251671
    Consensus CDS
    CCDS1248.1
    UniProtKB/Swiss-Prot
    P48443
    UniProtKB/TrEMBL
    F1D8Q7
    Related
    ENSP00000352900.5, ENST00000359842.10
    Conserved Domains (3) summary
    cd06943
    Location:233441
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:137213
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:25133
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

RNA

  1. NR_033824.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains the same 5' exon but lacks the remaining exons, and instead includes an alternate 3' exon, compared to variant 1. It is represented as non-coding because it lacks the majority of the coding region found in variant 1.
    Source sequence(s)
    BM684530, BX118484
    Related
    ENST00000465764.1

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    165400922..165445355 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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